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ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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multiple entries of FoodTroph for a species #177

Closed andybeet closed 1 year ago

andybeet commented 4 years ago

I am obtaining multiple values for FoodTroph in the ecology table

rfishbase::ecology(species_list="Oncorhynchus clarkii", server = "fishbase") %>% dplyr::select(Species,DietTroph,FoodTroph)

results in:

Species DietTroph FoodTroph

1 Oncorhynchus clarkii NA 3.77 2 Oncorhynchus clarkii NA 4.01 Is this a bug or a data entry issue in fishbase? I also see a value of 4.01 in the `estimate` table
Session Info ```r R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] magrittr_1.5 loaded via a namespace (and not attached): [1] Rcpp_1.0.2 rstudioapi_0.10 hms_0.5.1 tidyselect_0.2.5 [5] R6_2.4.0 rlang_0.4.0 fansi_0.4.0 stringr_1.4.0 [9] httr_1.4.1 dplyr_0.8.3 tools_3.6.1 utf8_1.1.4 [13] cli_1.1.0 indexPPR_0.1.0 assertthat_0.2.1 digest_0.6.20 [17] tibble_2.1.3 crayon_1.3.4 purrr_0.3.2 readr_1.3.1 [21] vctrs_0.2.0 curl_4.0 zeallot_0.1.0 memoise_1.1.0 [25] glue_1.3.1 gh_1.0.1 stringi_1.4.3 compiler_3.6.1 [29] pillar_1.4.2 backports_1.1.4 rfishbase_3.0.4 jsonlite_1.6 [33] pkgconfig_2.0.2 ```
sckott commented 4 years ago

I don't know is the short answer.

The species page https://www.fishbase.de/summary/2688 has the stockcode 2884, and the value 3.77 . Not sure why the other entry is there.

@cboettig ?

cboettig commented 1 year ago

clearing out some old issues here, apologies.

It's usually best to compare to the whole table, e.g. 

ecology(species_list="Oncorhynchus clarkii", server = "fishbase")

Note that this species includes multiple unique stocks (different populations). Important to remember that not all fishbase data is collated to the species level, and some tables involve individuals (eg. diet() ).